title: Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile.
abstract: The first step of the hydrolytic deimination of L-arginine catalyzed by arginine deiminase is examined using ab initio quantum mechanical/molecular mechanical molecular dynamics simulations. Two possible protonation states of the nucleophilic Cys406 residue were investigated, and the corresponding activation free energies were obtained via umbrella sampling. Our calculations indicated a reaction free-energy barrier of 21.3 kcal/mol for the neutral cysteine, which is in reasonably good agreement with the experimental k(cat) value of 6.3 s(-1), i.e., a barrier of 16.7 kcal/mol. On the other hand, the deprotonated Cys nucleophile yields a free-energy barrier of 6.7 kcal/mol, much lower than the experimental result. The reaction free-energy barriers along with other data suggest that the Cys nucleophile is dominated by its protonated state in the Michaelis complex, and the reaction barrier corresponds largely to its deprotonation.
authors.affiliation: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Ke
authors.forename: Hua
authors.initials: H
authors.lastname: Guo
authors.forename: Daiqian
authors.initials: D
authors.lastname: Xie
authors.forename: Shenglong
authors.initials: S
authors.lastname: Wang
authors.forename: Yingkai
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D003545:Cysteine / Q000737:chemistry*; D006867:Hydrolases / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011522:Protons; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D011522:Protons; D006867:Hydrolases; C019723:arginine deiminase; D003545:Cysteine